Dictionary size problem in Picard CalculateHsMetrics

Question

[nicola.licheri]

Hi everyone,

I'm following a Roche pipeline for the analysis of targeted bisulfite sequencing data and I'm in trouble with Picard CalculateHsMetrics.

I create the indexed reference file with samtools faidx command and the indexed .bam with samtools index.

When I run Picard, with the following command

java -Xmx4g -Xms4g -jar ~/bioTool/picard-tools-2.2.1/picard.jar CalculateHsMetrics BAIT_INTERVALS=DESIGN_bait_intervals.txt TARGET_INTERVALS=DESIGN_target_intervals.txt INPUT=2101435_S8_L001.clipped.bam.bai OUTPUT=2101435_S8_L001_picard_hs_metrics.txt METRIC_ACCUMULATION_LEVEL=ALL_READS REFERENCE_SEQUENCE=~/Data/MethylSeq/genomes/GRCh37_latest_genomic_idx.fa  VALIDATION_STRINGENCY=LENIENT TMP_DIR=.

it terminates with the following exception:

Exception in thread "main" htsjdk.samtools.util.SequenceUtil$SequenceListsDifferException: Sequence dictionaries are not the same size (0, 297)
    at htsjdk.samtools.util.SequenceUtil.assertSequenceListsEqual(SequenceUtil.java:188)
    at htsjdk.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:271)
    at htsjdk.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:257)
    at picard.analysis.directed.CollectTargetedMetrics.doWork(CollectTargetedMetrics.java:114)
    at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:209)
    at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
    at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)

It seems like there is a problem in the indexes, but I cannot figure it out.

Answer 1

[finswimmer]

Hello nicola,

you are passing the bam index file (bam.bai) to picard. But this have to be the bam file itsself.

fin swimmer

[nicola.licheri]

Awesome!! Thank you!

[finswimmer]

You're very welcome.

Please mark the answer as accepted if this solve your problem.

fin swimmer